LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-739-g2644e7f6fa-modified)
  using 1 OpenMP thread(s) per MPI task

units		real
atom_style	full

read_data	data.spce
Reading data file ...
  orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
  2 by 2 by 1 MPI processor grid
  reading atoms ...
  4500 atoms
  scanning bonds ...
  2 = max bonds/atom
  scanning angles ...
  1 = max angles/atom
  orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
  2 by 2 by 1 MPI processor grid
  reading bonds ...
  3000 bonds
  reading angles ...
  1500 angles
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     2 = max # of 1-2 neighbors
     1 = max # of 1-3 neighbors
     1 = max # of 1-4 neighbors
     2 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.014 seconds

pair_style	lj/cut/coul/long 12.0 12.0
kspace_style	pppm 1.0e-4

pair_coeff	1 1 0.15535 3.166
pair_coeff	* 2 0.0000 0.0000

bond_style	harmonic
angle_style	harmonic
dihedral_style	none
improper_style	none

bond_coeff	1 1000.00 1.000
angle_coeff	1 100.0 109.47

special_bonds   lj/coul 0.0 0.0 1.0
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        1       
  special bond factors coul:  0        0        1       
     2 = max # of 1-2 neighbors
     1 = max # of 1-3 neighbors
     2 = max # of special neighbors
  special bonds CPU = 0.000 seconds

neighbor        2.0 bin

fix		1 all shake 0.0001 20 0 b 1 a 1
Finding SHAKE clusters ...
       0 = # of size 2 clusters
       0 = # of size 3 clusters
       0 = # of size 4 clusters
    1500 = # of frozen angles
  find clusters CPU = 0.000 seconds
fix		2 all nvt temp 300.0 300.0 100.0

# make certain that shake constraints are satisfied
run 0 post no
PPPM initialization ...
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.21848247
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.031943453
  estimated relative force accuracy = 9.619676e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 3380 960
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 14
  ghost atom cutoff = 14
  binsize = 7, bins = 6 6 6
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.94 | 10.95 | 10.96 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   0             -16692.358      0             -16692.358     -1289.8319    
Loop time of 1.2025e-06 on 4 procs for 0 steps with 4500 atoms


group		one molecule 1 2
6 atoms in group one

# the following section shows equivalences between using the stress/tally compute and other computes and thermo keywords

# compute per atom stress contributions
compute		spa all stress/atom NULL pair
compute		press all pressure NULL pair
# compute stress contributions from one group with all
compute		c1 one stress/tally all
# collect stress contributions from all with all
compute		c2 all stress/tally all
compute		one one reduce sum c_c1[1] c_c1[2] c_c1[3] c_spa[1] c_spa[2] c_spa[3]
compute		red all reduce sum c_spa[1] c_spa[2] c_spa[3] c_c2[1] c_c2[2] c_c2[3]
#
variable	spa equal -(c_red[1]+c_red[2]+c_red[3])/(3.0*vol)
variable	press equal -(c_red[4]+c_red[5]+c_red[6])/(3.0*vol)
variable	one equal (c_one[1]+c_one[2]+c_one[3])/3.0
variable	ref equal (c_one[4]+c_one[5]+c_one[6])/3.0

#velocity	all create 300 432567 dist uniform

timestep	2.0

thermo_style    custom step c_press v_spa v_press v_one v_ref
thermo		10

run 50
PPPM initialization ...
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.21848247
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.031943453
  estimated relative force accuracy = 9.619676e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 3380 960
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Compute stress/tally only called from pair style (src/TALLY/compute_stress_tally.cpp:79)
WARNING: Compute stress/tally only called from pair style (src/TALLY/compute_stress_tally.cpp:79)
Per MPI rank memory allocation (min/avg/max) = 15.64 | 15.65 | 15.66 Mbytes
   Step        c_press         v_spa         v_press         v_one          v_ref     
         0   26496.811      26496.811      26496.811     -2356992.8     -2356992.8    
        10   23665.129      23665.129      23665.129     -2096058.5     -2096058.5    
        20   23338.197      23338.197      23338.197     -2034283.9     -2034283.9    
        30   25946.434      25946.434      25946.434     -2002815.2     -2002815.2    
        40   27238.373      27238.373      27238.373     -2155408.5     -2155408.5    
        50   27783.106      27783.106      27783.106     -1862191.9     -1862191.9    
Loop time of 0.379763 on 4 procs for 50 steps with 4500 atoms

Performance: 22.751 ns/day, 1.055 hours/ns, 131.661 timesteps/s, 592.474 katom-step/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.30496    | 0.31222    | 0.32527    |   1.4 | 82.21
Bond    | 0.00027957 | 0.00028771 | 0.00030283 |   0.0 |  0.08
Kspace  | 0.01621    | 0.029213   | 0.036476   |   4.5 |  7.69
Neigh   | 0.023535   | 0.023563   | 0.023582   |   0.0 |  6.20
Comm    | 0.0044831  | 0.0045405  | 0.0045746  |   0.1 |  1.20
Output  | 0.0032277  | 0.0032389  | 0.0032701  |   0.0 |  0.85
Modify  | 0.0060353  | 0.006043   | 0.0060504  |   0.0 |  1.59
Other   |            | 0.0006619  |            |       |  0.17

Nlocal:           1125 ave        1154 max        1092 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Nghost:        12263.5 ave       12300 max       12219 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs:         650438 ave      678787 max      626279 min
Histogram: 1 0 0 1 1 0 0 0 0 1

Total # of neighbors = 2601750
Ave neighs/atom = 578.16667
Ave special neighs/atom = 2
Neighbor list builds = 3
Dangerous builds = 0

Total wall time: 0:00:00
